single-cell pipeline

scRNA-seq data

Result

# library(dplyr)

BA-1_209_NormR_rna

QC metrics of cells before QC filtering

QC metrics of cells after QC filtering

Doublet detection

UMAP Clustering by cluster numbers

Celltype annotation based on breast markers

Heatmap of differentially expressed genes across annotated celltypes

Gene expression levels of breast atlas markers

Gene expression levels of immune cell markers

GSEA hallmark by cluster

BA-8_374_NormL_rna

QC metrics of cells before QC filtering

QC metrics of cells after QC filtering

Doublet detection

UMAP Clustering by cluster numbers

Celltype annotation based on breast markers

Heatmap of differentially expressed genes across annotated celltypes

Gene expression levels of breast atlas markers

Gene expression levels of immune cell markers

GSEA hallmark by cluster

BI54_rna

QC metrics of cells before QC filtering

QC metrics of cells after QC filtering

Doublet detection

UMAP Clustering by cluster numbers

Celltype annotation based on breast markers

Heatmap of differentially expressed genes across annotated celltypes

Gene expression levels of breast atlas markers

Gene expression levels of immune cell markers

GSEA hallmark by cluster

MGH23039R_rna

QC metrics of cells before QC filtering

QC metrics of cells after QC filtering

Doublet detection

UMAP Clustering by cluster numbers

Celltype annotation based on breast markers

Heatmap of differentially expressed genes across annotated celltypes

Gene expression levels of breast atlas markers

Gene expression levels of immune cell markers

GSEA hallmark by cluster

merge_1

UMAP by samples before integration

UMAP by samples after batch correction

Celltype annotation based on breast markers

Heatmap of differentially expressed genes across annotated celltypes

Heatmap of differentially expressed genes across annotated celltypes

Gene expression levels of breast atlas markers

Gene expression levels of immune cell markers

merge_2

UMAP by samples before integration

UMAP by samples after batch correction

Celltype annotation based on breast markers

Heatmap of differentially expressed genes across annotated celltypes

Heatmap of differentially expressed genes across annotated celltypes

Gene expression levels of breast atlas markers

Gene expression levels of immune cell markers

scATAC-seq data

Result

B1_7218

QC metrics of cells before QC filtering

QC metrics of cells after QC filtering

UMAP Clustering by cluster numbers

UMAP Clustering by scATAnno Annotation

B2_7157

QC metrics of cells before QC filtering

QC metrics of cells after QC filtering

UMAP Clustering by cluster numbers

UMAP Clustering by scATAnno Annotation

M1_atac

QC metrics of cells before QC filtering

QC metrics of cells after QC filtering

UMAP Clustering by cluster numbers

UMAP Clustering by scATAnno Annotation

M2_atac

QC metrics of cells before QC filtering

QC metrics of cells after QC filtering

UMAP Clustering by cluster numbers

UMAP Clustering by scATAnno Annotation

merge_1

UMAP by scATAC samples before integration

UMAP by scATAC samples after batch correction

UMAP Clustering by scATAnno Annotation

merge_2

UMAP by scATAC samples before integration

UMAP by scATAC samples after batch correction

UMAP Clustering by scATAnno Annotation

scRNA-scATAC integration

Result

merge_1

UMAP integration by assays

UMAP integration by samples

UMAP integration by celltypes

merge_2

UMAP integration by assays

UMAP integration by samples

UMAP integration by celltypes